It's just saying that it's giving you back a dataset that tells you
where the brain is (which you requested with -mask_vol) instead of giving back a dataset that's just the brain (which is what you'd get with -orig_vol). From the help:
-norm_vol: Output a masked and somewhat intensity normalized and
thresholded version of the input. This is the default,
and you can use -orig_vol to override it.
-orig_vol: Output a masked version of the input AND do not modify
the values inside the brain as -norm_vol would.
-mask_vol: Output a mask volume instead of a skull-stripped
volume.
The mask volume containes:
0: Voxel outside surface
1: Voxel just outside the surface. This means the voxel
center is outside the surface but inside the
bounding box of a triangle in the mesh.
2: Voxel intersects the surface (a triangle), but center
lies outside.
3: Voxel contains a surface node.
4: Voxel intersects the surface (a triangle), center lies
inside surface.
5: Voxel just inside the surface. This means the voxel
center is inside the surface and inside the
bounding box of a triangle in the mesh.
6: Voxel inside the surface.
